Who is Who in Phylogenetic Networks

Publications of David A. Morrison     Order by:   Type | Year

Associated keywords

abstract-network database explicit-network from-network from-NGS-data from-unrooted-trees hybridization median-network NeighborNet phylogenetic-network phylogeny population-genetics Program-Network Program-Spectronet Program-SplitsTree Program-T-REX Program-TCS recombination reconstruction reticulogram split-decomposition split-network survey visualization

Article (Journal)

1 Klaus Schliep, Alastair J. Potts, David A. Morrison and Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):1212-1220, 2017. Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization. Note: http://dx.doi.org/10.1111/2041-210X.12760.         2 David A. Morrison. Phylogenetic Networks: A Review of Methods to Display Evolutionary History. In Annual Research & Review in Biology, Vol. 4(10):1518-1543, 2014. Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.         3 David A. Morrison. Rooted Phylogenetic Networks for Exploratory Data Analysis. In Advances in Research, Vol. 2(3):145-152, 2014. Keywords: abstract network, explicit network, phylogenetic network, reconstruction.         4 David A. Morrison. Next generation sequencing and phylogenetic networks. In EMBnet.journal, Vol. 20(e760):1-4, 2014. Keywords: abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.         5 David A. Morrison. Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics? In Systematic Biology, Vol. 63(4):628-638, 2014. Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.         6 Eric Bapteste, Leo van Iersel, Axel Janke, Scott Kelchner, Steven Kelk, James O. McInerney, David A. Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James B. Whitfield. Networks: expanding evolutionary thinking. In Trends in Genetics, Vol. 29(8):439-441, 2013. Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction. Note: http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf.         Toggle abstract "Networks allow the investigation of evolutionary relationships that do not fit a tree model. They are becoming a leading tool for describing the evolutionary relationships between organisms, given the comparative complexities among genomes. © 2013 Elsevier Ltd." 7 David A. Morrison. Using data-display networks for exploratory data analysis in phylogenetic studies. In MBE, Vol. 27(5):1044-1057, 2010. Keywords: abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition. Note: http://dx.doi.org/10.1093/molbev/msp309.         Toggle abstract "Exploratory data analysis (EDA) is a frequently undervalued part of data analysis in biology. It involves evaluating the characteristics of the data "before" proceeding to the definitive analysis in relation to the scientific question at hand. For phylogenetic analyses, a useful tool for EDA is a data-display network. This type of network is designed to display any character (or tree) conflict in a data set, without prior assumptions about the causes of those conflicts. The conflicts might be caused by 1) methodological issues in data collection or analysis, 2) homoplasy, or 3) horizontal gene flow of some sort. Here, I explore 13 published data sets using splits networks, as examples of using data-display networks for EDA. In each case, I performed an original EDA on the data provided, to highlight the aspects of the resulting network that will be important for an interpretation of the phylogeny. In each case, there is at least one important point (possibly missed by the original authors) that might affect the phylogenetic analysis. I conclude that EDA should play a greater role in phylogenetic analyses than it has done. © 2010 The Author. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved." 8 David A. Morrison. Networks in phylogenetic analysis: new tools for population biology. In IJP, Vol. 35:567-582, 2005. Keywords: median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey. Note: http://hem.fyristorg.com/acacia/papers/networks.pdf.

InBook

9 David A. Morrison. Phylogenetic networks are fundamentally different from other kinds of biological networks. In WenJun Zhang editor, Network Biology: Theories, Methods and Applications, Chapter 2, Nova Publishers, 2013. Keywords: abstract network, explicit network, phylogenetic network, phylogeny.         10 David A. Morrison. Phylogenetic networks in systematic biology (and elsewhere) In R.M. Mohan editor, Research Advances in Systematic Biology, Global Research Network, Trivandrum, India, 2010. Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction, survey.

Misc

11 Steven Kelk, Simone Linz and David A. Morrison. Fighting network space: it is time for an SQL-type language to filter phylogenetic networks. 2013. Keywords: database, explicit network, from network, phylogenetic network, phylogeny. Note: http://arxiv.org/abs/1310.6844.         12 David A. Morrison, Leo van Iersel and Steven Kelk. The Genealogical World of Phylogenetic Networks. Blog, 2012. Keywords: survey. Note: http://phylonetworks.blogspot.com/.

Book

13 David A. Morrison. Introduction to Phylogenetic Networks. RJR Productions, 2011. Keywords: phylogenetic network, phylogeny, reconstruction, survey. Note: http://www.rjr-productions.org/Networks/Download.html.